Simulation of Self Assembly

This page lists publications on self assembly that have arisen directly from the Programme Grant. For the complete publication lists of individual members of the collaboration, please follow links to their personal home pages from the People tab.

	A threshold-minimization scheme for exploring the energy landscape of biomolecules: application to a cyclic peptide and a disaccharide S. Neelamraju, R. L. Johnston and J. C. Schön Journal of Chemical Theory and Computation, (2016)
	Design principles for rapid folding of knotted DNA nanostructures V. Kočar, J. S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J. P. K. Doye, and R. Jerala Nature Communications, 7, 10803 (2016) [Open access]
	Direct simulation of the self-assembly of a small DNA origami B. E. K. Snodin, F. Romano, L. Rovigatti, T. E. Ouldridge, A. A. Louis and J. P. K. Doye ACS Nano, 10, 1724 (2016)
	Force-induced rupture of a DNA duplex: From fundamentals to force sensors M. Mosayebi, A. A. Louis, J. P. K. Doye and T. E. Ouldridge ACS Nano, 9, 11993 (2015)
	Chiral effects on helicity studied via the energy landscape of short (D,L)-alanine peptides S. Neelamraju, M. T. Oakley and R. L. Johnston Journal of Chemical Physics, 143, 165103 (2015)
	Percolation in suspensions of hard nanoparticles: From spheres to needles T. Schilling, M. A. Miller and P. van der Schoot Europhysics Letters, 111, 56004 (2015) [Preprint]
	Design strategies for self-assembly of discrete targets J. Madge and M. A. Miller Journal of Chemical Physics, 143, 044905 (2015) [Preprint]
	DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. P. Shaw, A. A. Louis and J. P. K. Doye Nucleic Acids Research, 43, 6181-6190 (2015) [Open access]
	Intrinsically disordered energy landscapes Y. Chebaro, A. J. Ballard, D. Chakraborty and D. J. Wales Scientific Reports, 5, 10386 (2015)
	Equilibrium molecular thermodynamics from Kirkwood sampling S. Somani, Y. Okamoto, A. J. Ballard and D. J. Wales Journal of Physical Chemistry B, 119, 6155-6169 (2015)
	Rational design of self-assembly pathways for complex multicomponent structures W. M. Jacobs, A. Reinhardt and D. Frenkel Proceedings of the National Academy of Sciences USA, 112, 6313-6318 (2015)
	Designing multivalent probes for tunable superselective targeting G. V. Dubacheva, T. Curk, R. Auzely-Velty, D. Frenkel and R. P. Richter Proceedings of the National Academy of Sciences USA, 112, 5579-5584 (2015)
	Introducing improved structural properties and salt dependence into a coarse-grained model of DNA B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis and J. P. K. Doye Journal of Chemical Physics, 142, 234901 (2015)
	Characterizing the bending and flexibility induced by bulges in DNA duplexes J. S. Schreck, F. Romano, T. E. Ouldridge, A. A. Louis and J. P. K. Doye Journal of Chemical Physics, 142, 165101 (2015) [Preprint]
	Structures and energy landscapes of hydrated sulfate clusters L. C. Smeeton, J. D. Farrell, M. T. Oakley, D. J. Wales and R. L. Johnston Journal of Chemical Theory and Computation, 11 2377-2384 (2015) [Open access]
	Modelling toehold-mediated RNA strand displacement P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye and A. A. Louis Biophysical journal, 108, 1238-1247 (2015)
	Theoretical prediction of free-energy landscapes for complex self-assembly W. M. Jacobs, A. Reinhardt and D. Frenkel Journal of Chemical Physics, 142, 021101 (2015)
	Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA C. Matek, T. E. Ouldridge, J. P. K. Doye and A. A. Louis Scientific Reports, 5, 7655 (2015) [Open access]
	Superposition-enhanced estimation of optimal temperature spacings for parallel tempering simulations A. J. Ballard and D. J. Wales Journal of Chemical Theory and Computation, 10, 5599-5605 (2014)
	Exploring energy landscapes: From molecular to mesoscopic systems D. Chakrabarti, H. Kusumaatmaja, V. Rühle and D. J. Wales Physical Chemistry Chemical Physics, 16, 5014-5025 (2014)
	Observation time scale, free energy landscapes, and molecular symmetry D. J. Wales and P. Salamon Proceedings of the National Academy of Sciences USA, 111, 617-622 (2014)
	The role of loop stacking in the dynamics of DNA hairpin formation M. Mosayebi, F. Romano, T. E. Ouldridge, A. A. Louis and J. P. K. Doye Journal of Physical Chemistry B, 118, 14326-14335 (2014) [Preprint]
	Heterogeneous ice nucleation on silver-iodide-like surfaces G. Fraux and J. P. K. Doye Journal of Chemical Physics, 141, 216101 (2014) [Preprint]
	Optimizing the selectivity of surface-adsorbing multivalent polymers N. B. Tito and D. Frenkel Macromolecules, 47, 7496-7509 (2014)
	Mobile linkers on DNA-coated colloids: Valency without patches S. Angioletti-Uberti, P. Varilly, B. M. Mognetti and D. Frenkel Physical Review Letters, 113, 128303 (2014) [Preprint]
	Superposition enhanced nested sampling S. Martiniani, J. D. Stevenson, D. J. Wales and D. Frenkel Physical Review X, 4, 031034 (2014)
	Effects of surface interactions on heterogeneous ice nucleation for a monatomic water model A. Reinhardt and J. P. K. Doye Journal of Chemical Physics, 141, 084501 (2014) [Preprint]
	Crucial role of nonspecific interactions in amyloid nucleation A. Šarić, Y. C. Chebaro, T. P. J. Knowles and D. Frenkel Proceedings of the National Academy of Sciences USA, 111, 17869-17874 (2014)
	Simulating a burnt-bridges DNA motor with a coarse-grained DNA model P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye and A. A. Louis Natural Computing, 13, 535-547 (2014) [Preprint]
	Clusters of coarse-grained water molecules J. D. Farrell and D. J. Wales Journal of Physical Chemistry A 118 7338-7348 (2014) [Preprint]
	A nucleotide-level coarse-grained model of RNA P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye and A. A. Louis Journal of Chemical Physics 140 235102 (2014) [Preprint]
	Potential energy landscape of the two-dimensional XY model: Higher-index stationary points D. Mehta, C. Hughes, M. Kastner, and D. J. Wales Journal of Chemical Physics 140 224503 (2014)
	Design principles for Bernal spirals and helices with tunable pitch S. N. Fejer, D. Chakrabarti, H. Kusumaatmaja and D. J. Wales Nanoscale (2014)
	Visualizing energy landscapes with metric disconnectivity graphs L. C. Smeeton, M. T. Oakley and R. L. Johnston Journal of Computational Chemistry 35 1481--1490 (2014) [Open access]
	Numerical evidence for nucleated self-assembly of DNA brick structures A. Reinhardt and D. Frenkel Physical Review Letters 112 238103 (2014)
	Phase separation in solutions with specific and nonspecific interactions W. M. Jacobs, D. W. Oxtoby and D. Frenkel Journal of Chemical Physics 140 204109 (2014)
	Effect of inert tails on the thermodynamics of DNA hybridization L. Di Michele, B. M. Mognetti, T. Yanagishima, P. Varilly, Z. Ruff, D. Frenkel and E. Eiser Journal of the American Chemical Society 136 6538--6541 (2014)
	An inversion-relaxation approach for sampling stationary points of spin model Hamiltonians C. Hughes, D. Mehta, and D. J. Wales Journal of Chemical Physics 140 194104 (2014)
	New metastable form of ice and its role in the homogeneous crystallization of water J. Russo, F. Romano and H. Tanaka Nature Materials 13 733-739 (2014)
	Gels of DNA nanostars never crystallize L. Rovigatti, F. Smallenburg, F. Romano and F. Sciortino ACS Nano 8 3567-3574 (2014)
	A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly B. Barz, D. J. Wales and B. Strodel Journal of Physical Chemistry B 118 1003-1011 (2014)
	Chemistry, geometry, and defects in two dimensions D. J. Wales ACS Nano 8 1081-1085 (2014)
	A conformational factorisation approach for estimating the binding free energies of macromolecules K. Mochizuki, C. S. Whittleston, S. Somani, H. Kusumaatmaja and D. J. Wales Physical Chemistry Chemical Physics 16 2842-2853 (2014)
	Stability of bicelles: A simulation study R. Vacha and D. Frenkel Langmuir 30 4229-4235 (2014)
	Energy landscapes and global optimisation of self-assembling cyclic peptides M. T. Oakley and R. L. Johnston Journal of Chemical Theory and Computation 10 1810-1816 (2014)
	Simulations suggest possible novel membrane pore structure R. Vacha and D. Frenkel Langmuir 30 1304-1310 (2014)
	Designing stimulus-sensitive colloidal walkers F. J. Martinez-Veracoechea, B. M. Mognetti, S. Anglioletti-Uberti, P. Varilly, D. Frenkel and J. Dobnikar Soft Matter 10 3463-3470 (2014)
	Depletion-interaction effects on the tunneling conductivity of nanorod suspensions B. Nigro, C. Grimaldi, M. A. Miller, P. Ryser and T. Schilling Physical Review E 88 042140 (2013) [Preprint]
	Predicting phase behavior in multicomponent mixtures W. M. Jacobs and D. Frenkel Journal of Chemical Physics 139 024108 (2013)
	Visualizing basins of attraction for different minimization algorithms D. Asenjo, J. D. Stevenson, D. J. Wales and D. Frenkel Journal of Physical Chemistry B 117 12717-12723 (2013)
	Designing a Bernal spiral from patchy colloids J. W. R. Morgan, D. Chakrabarti, N. Dorsaz and D. J. Wales ACS Nano 7 1246-1256 (2013)
	A simple analytical formula for the free energy of ligand-receptor-mediated interactions S. Angioletti-Uberti, P. Varilly, B. M. Mognetti, A. V. Tkachenko and D. Frenkel Journal of Chemical Physics 138 021102 (2013)
	Procedure to construct a multi-scale coarse-grained model of DNA-coated colloids from experimental data B. M. Mladek, J. Fornleitner, F. J. Martinez-Veracoechea, A. Dawid and D. Frenkel Soft Matter 9 7342-7355 (2013)
	Surveying a complex potential energy landscape: Overcoming broken ergodicity using basin-sampling D. J. Wales Chemical Physics Letters 584 1-9 (2013)
	Exploring energy landscapes: Metrics, pathways, and normal-mode analysis for rigid-body molecules V. Rühle, H. Kusumaatmaja, D. Chakrabarti and D. J. Wales Journal of Chemical Theory and Computation 9 4026-4034 (2013) [Preprint]
	Potential energy landscapes for the 2D XY model: Minima, transition states and pathways D. Mehta, C. Hughes, M. Schroeck and D. J. Wales Journal of Chemical Physics 139 194503 (2013)
	Protein Structure Optimisation With a "Lamarckian" Ant Colony Algorithm M. T. Oakley, E. G. Richardson, H. Carr and R. L. Johnston IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 1548-1552 (2013)
	On the biophysics and kinetics of toehold-mediated DNA strand displacement N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye and E. Winfree Nucleic Acids Research 41 10641-10658 (2013) [Open access]
	The other entropy D. Frenkel, D. Asenjo and F. Paillusson Molecular Physics 111 3641-3650 (2013)
	Homogeneous TIP4P/2005 ice nucleation at low supercooling A. Reinhardt and J. P. K. Doye Journal of Chemical Physics 139 096102 (2013) [Preprint]
	Coarse-graining DNA for simulations of DNA nanotechnology J. P. K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B. E. K. Snodin, L. Rovigatti, J. S. Schreck, R. M. Harrison and W. P. J. Smith Physical Chemistry Chemical Physics 15 20395-20414 (2013) [Preprint]
	Symmetrisation schemes for global optimisation of atomic clusters M. T. Oakley, R. L. Johnston and D. J. Wales Physical Chemistry Chemical Physics 15 3965-3976 (2013)
	Computational and experimental investigations into the conformations of cyclic tetra-α/β-peptides M. T. Oakley, E. Oheix, A. F. A. Peacock and R. L. Johnston Journal of Physical Chemistry B 117 8122-8134 (2013)
	DNA hybridization kinetics: zippering, internal displacement and sequence dependence T. E. Ouldridge, P. Šulc, F. Romano, J. P. K. Doye and A. A. Louis Nucleic Acids Research 41 8886-8895 (2013) [Open access]
	Computing phase diagrams for a quasicrystal-forming patchy-particle system A. Reinhardt, F. Romano and J. P. K. Doye Physical Review Letters 110 255503 (2013) [Preprint]
	Energy landscapes, structural topologies and rearrangement mechanisms in clusters of dipolar particles J. D. Farrell, C. Lines, J. J. Shepherd, D. Chakrabarti, M. A. Miller and D. J. Wales Soft Matter 9 5407-5416 (2013) [Open access]
	Optimizing DNA nanotechnology through coarse-grained modelling: A two-footed DNA walker T. E. Ouldridge, R. Hoare, A. A. Louis, J. P. K. Doye, J. Bath and A. J. Turberfield ACS Nano 7 2479-2490 (2013)
	Coarse-grained simulations of DNA overstretching F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge and A. A. Louis Journal of Chemical Physics 138 085101 (2013) [Preprint]
	Simulations: The dark side D. Frenkel European Physical Journal Plus 128 10 (2013)
	Exploring the energy landscapes of cyclic tetrapeptides with discrete path sampling M. T. Oakley and R. L. Johnston Journal of Chemical Theory and Computation 9 650-657 (2013)
	Defect motifs for constant mean curvature surfaces H. Kusumaatmaja and D. J. Wales Physical Review Letters 110 165502 (2013) [Preprint]
	Density functional theory for Baxter's sticky hard spheres in confinement H. Hansen-Goos, M. A. Miller and J. S. Wettlaufer Physical Review Letters 108 047801 (2012) [Preprint]
	A local rigid body framework for global optimization of biomolecules H. Kusumaatmaja, C. S. Whittleston and D. J. Wales Journal of Chemical Theory and Computation 8 5159-5165 (2012) [Preprint]
	Tunneling conductivity in composites of attractive colloids B. Nigro, C. Grimaldi, M. A. Miller, P. Ryser and T. Schilling Journal of Chemical Physics 136 164903 (2012) [Preprint]
	Quasi-continuous interpolation scheme for pathways between distant configurations D. J. Wales and J. M. Carr Journal of Chemical Chemical Theory and Computation 8 5020-5034 (2012)
	Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water A. Reinhardt, J. P. K. Doye, E. G. Noya and C. Vega Journal of Chemical Physics 137 194504 (2012) [Preprint]
	Sequence-dependent thermodynamics of a coarse-grained DNA model P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye and A. A. Louis Journal of Chemical Physics B 137 135101 (2012) [Preprint]
	DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye and A. A. Louis Journal of Physical Chemistry B 116 11616 (2012) [Preprint]
	Vacancy-stabilized crystalline order in hard cubes F. Smallenburg, L. Filion, M. Marechal and M. Dijkstra Proceedings of the National Academy of Sciences USA 109 17886-17890 (2012) [Preprint]
	Running faster together: Huge speed up of thermal ratchets due to hydrodynamic coupling P. Malgaretti, I. Pagonabarraga and D. Frenkel Physical Review Letters 109 168101 (2012)
	Connecting macroscopic observables and microscopic assembly events in amyloid formation using coarse grained simulations N. S. Bieler, T. P. J. Knowles, D. Frenkel and R. Vacha PLOS Computational Biology 8 e1002692 (2012) [Open access]
	Quantitative prediction of the phase diagram of DNA-functionalized nanosized colloids B. M. Mladek, J. Fornleitner, F. J. Martinez-Veracoechea, A. Dawid and D. Frenkel Physical Review Letters 108 268301 (2012)
	A parameter-free, solid-angle based, nearest-neighbor algorithm J. A. van Meel, L. Filion, C. Valeriani and D. Frenkel Journal of Chemical Physics 136 234107 (2012)
	Re-entrant melting as a design principle for DNA-coated colloids S. Angioletti-Uberti, B. M. Mognetti and D. Frenkel Nature Materials 11 518-522 (2012)
	Intrinsic disorder modulates protein self-assembly and aggregation A. De Simone, C. Kitchen, A. H. Kwan, M. Sunde, C. M. Dobson and D. Frenkel Proceedings of the National Academy of Sciences USA 109 6951-6956 (2012)
	Layering, freezing, and re-entrant melting of hard spheres in soft confinement T. Curk, A. de Hoogh, F. J. Martinez-Veracoechea, E. Eiser, D. Frenkel, J. Dobnikar and M. E. Leunissen Physical Review E 85 021502 (2012)
	Controlling the folding and substrate-binding of proteins using polymer brushes B. M. Rubenstein, I. Coluzza and M. A. Miller Physical Review Letters 108 208104 (2012) [Preprint]
	The effect of topology on the structure and free energy landscapes of DNA kissing complexes F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge and A. A. Louis Journal of Chemical Physics 136 215102 (2012) [Preprint]
	The effect of nonnative interactions on the energy landscapes of frustrated model proteins M. T. Oakley, D. J. Wales and R. L. Johnston Journal of Atomic, Molecular and Optical Physics 2012 192613 (2012) [Open access]
	Effect of interaction specificity on the phase behaviour of patchy particles N. Dorsaz, L. Filion, F. Smallenburg and D. Frenkel Faraday Discussions 159 9-21 (2012)
	Formation of dodecagonal quasicrystals in two-dimensional systems of patchy particles M. N. van der Linden, J. P. K. Doye and A. A. Louis Journal of Chemical Physics 136 054904 (2012) [Preprint]
	Energy landscapes of colloidal clusters: Thermodynamics and rearrangement mechanisms F. Calvo, J. P. K. Doye and D. J. Wales Nanoscale 4 1085-1100 (2011)
	Energy landscape and global optimisation for a frustrated model protein M. T. Oakley, D. J. Wales and R. L. Johnston Journal of Physical Chemistry B 115 11525 (2011) [Open access]
	Colloidal self-assembly: Designed to yield D. Frenkel and D. J. Wales Nature Materials 10 410 (2011)